dilp {dilp}

Generate DiLP results

Description

dilp() processes raw leaf physiognomic data, checks for common errors/outliers, and returns the processed data, keys to finding potential errors or outliers, and paleoclimate reconstructions.

Usage

dilp(specimen_data, params = "PeppeGlobal", subsite_cols = NULL)

Arguments

specimen_data

A data frame containing specimen level leaf physiognomic data. See Lowe et al. 2024 for more information on how to collect this data. A good reference for how to put together the data: McAbeeExample

Required columns:

• site

• specimen_number

• morphotype

• margin

• feret

• blade_area

• raw_blade_perimeter

• internal_raw_blade_perimeter

• length_of_cut_perimeter

• no_of_primary_teeth

• no_of_subsidiary_teeth

Recommended columns:

• petiole_width

• petiole_area

• blade_perimeter

• minimum_feret

• raw_blade_area

• internal_raw_blade_area

params

Either a string referring to one of two preloaded parameter sets of a list of custom parameters (same format as the list below).

Preloaded parameter sets are "PeppeGlobal" and "PeppeNH" which are calibrated based on global and northern hemisphere data respectively. Allen et al. (2020) illustrates a situation in which the northern hemisphere parameters may be preferable. The "PeppeNH" parameters only estimate MAT. Use "PeppeGlobal" for all MAP estimates. Defaults to "PeppeGlobal" as follows (Peppe et al. 2011):

• MAT.MLR.M = 0.21,

• MAT.MLR.FDR = 42.296,

• MAT.MLR.TC.IP = -2.609,

• MAT.MLR.constant = -16.004,

• MAT.MLR.error = 4,

• MAT.SLR.M = 0.204,

• MAT.SLR.constant = 4.6,

• MAT.SLR.error = 4.9,

• MAP.MLR.LA = 0.298,

• MAP.MLR.TC.IP = 0.279,

• MAP.MLR.PR = -2.717,

• MAP.MLR.constant = 3.033,

• MAP.MLR.SE = 0.6,

• MAP.SLR.LA = 0.283,

• MAP.SLR.constant = 2.92,

• MAP.SLR.SE = 0.61

subsite_cols

A vector or list of columns present in specimen_data to calculate paleoclimate estimates for. A completely optional parameter - allows different groupings of specimens to be tested, or comparisons of paleoclimate estimates at different levels of grouping. Adds additional estimates to $results.

Value

A list of tables that includes all pertinent DiLP information:

• processed_leaf_data: the full set of cleaned and newly calculated leaf physiognomic data that is necessary for DiLP analysis. See dilp_processing() for more information.

• processed_morphotype_data: morphospecies-site pair means for all leaf physiognomic data.

• processed_site_data: site means for all leaf physiognomic data.

• errors: lists any specimens that may be causing common errors in DiLP calculations. See dilp_errors() for more information.

• outliers: flags outliers in variables used for DiLP analysis that may represent incorrect data. See dilp_outliers() for more information.

• results: climate reconstructions of MAT and MAP using single and multi-linear regressions.

References

• Allen, S. E., Lowe, A. J., Peppe, D. J., & Meyer, H. W. (2020). Paleoclimate and paleoecology of the latest Eocene Florissant flora of central Colorado, USA. Palaeogeography, Palaeoclimatology, Palaeoecology, 551, 109678.

• Peppe, D.J., Royer, D.L., Cariglino, B., Oliver, S.Y., Newman, S., Leight, E., Enikolopov, G., Fernandez-Burgos, M., Herrera, F., Adams, J.M., Correa, E., Currano, E.D., Erickson, J.M., Hinojosa, L.F., Hoganson, J.W., Iglesias, A., Jaramillo, C.A., Johnson, K.R., Jordan, G.J., Kraft, N.J.B., Lovelock, E.C., Lusk, C.H., Niinemets, Ü., Peñuelas, J., Rapson, G., Wing, S.L. and Wright, I.J. (2011), Sensitivity of leaf size and shape to climate: global patterns and paleoclimatic applications. New Phytologist, 190: 724-739. https://doi.org/10.1111/j.1469-8137.2010.03615.x

• Lowe. A.J., Flynn, A.G., Butrim, M.J., Baumgartner, A., Peppe, D.J., and Royer, D.L. (2024), Reconstructing terrestrial paleoclimate and paleoecology with fossil leaves using Digital Leaf Physiognomy and leaf mass per area. JoVE.

Examples

dilp_results <- dilp(McAbeeExample)
dilp_results$processed_leaf_data
dilp_results$processed_morphotype_data
dilp_results$processed_site_data
dilp_results$errors
dilp_results$outliers
dilp_results$results